PCR 'contamination' - (May/14/2007 )
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I strongly agree with tfitzwater. From your way of description, the less than 100bp bands should be primer-dimer.
Why not you lower the concentration of your primers in the PCR reaction?
could it be a primer concatemer ?
try decreasing your amount of primers in the reaction to see
i attached a gelîcture.
First lane is negative contrl and second is my pcr product.
You should see the primer dimers
This is problem should not be to hard to solve.
Use filtertips
Set up your PCR in a different room than were you are doing post-PCR procedures
Since you have already used your reagents in a post-PCR enviroment they could be contaminated with post PCR-products, and you should replace those reagents (including primers) with new ones
I can see that this have been suggested before, but I just want to emphasize it.
I don't think autoclaving does remove DNA by the way
What is your negative control ? It it your master mix (not add template) or only distill water ? If you use master mix as the negative control, I agree with other suggestions that it could be primer dimer. Decreasing the amount of primer will help you.
But if you use distill water as your negative control, it might be contaminated from your mixture, pipett tip, eppendorf tube ?
I don't think that you have to use filter tip. I never use it but my PCR is quite well. However, you have to ensure the sterility by autoclaving everything
Hope you sucessful
First lane is negative contrl and second is my pcr product.
You should see the primer dimers
Ya this is what I am talking. This time I have reduced the primer concentration and started to use separate bench so my problem is being solved.
Thanks all you are very helpful!